


Clash of the Shepard

by TheExecutioner0496



Category: Mass Effect
Genre: Alternate Universe, F/M, I always wanted to romance Joker, M/M, Mass Effect 3, Might add more tags later, Misuse of Biotics, So mad when I couldn't, Two Shepards at once, warnings just in case
Language: English
Status: Completed
Published: 2016-11-08
Updated: 2016-11-10
Packaged: 2018-08-29 20:30:21
Rating: Mature
Warnings: Graphic Depictions Of Violence
Chapters: 2
Words: 2,817
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/8504335
Author URL: https://archiveofourown.org/users/TheExecutioner0496/pseuds/TheExecutioner0496
Summary: During the events of Mass Effect 3 and after the attempted coop in the Citidel the Normandy and crew encounter a Wormhole during their travels and an alternate female version of John Shepard winds up on their ship. This woman, Jane Shepard, seems to be in a rather intimate relationship with the ship's pilot, has no idea why the hell Kaidan survived the mission on Virmire, and is a powerful human biotic. The crew is forced to work around the new addition to the crew while John and Jane Shepard start to clash whenever the encounter one another.





	1. Chapter 1

**Author's Note:**

> I encountered this idea while searching for Shakarian posts on Tumblr so it is most certainly not my idea at all. I simply wanted to take it into a different direction.

EDI had tried to help Joker steer the Normandy away from the Wormhole ahead of them but it ended up being a case of too little, too late. Instead a unstable... thing was detected in the Engineering deck and when John and Kaidan were sent to investigate all they found was an unknown redheaded woman, roughly five feet and five inches tall, wearing N7 armor, and looking eerily similar to John was talking to Tali in an animated tone. When the woman noticed John's presence, though, a biotic corona surrounded her and she threw a barrier up around both herself and the quarian before speaking up.   
"I'm Commander Shepard, Spectre and Commander for the Alliance Navy. Who the hell are you and wh-" She started what sounded like a rehearsed speech before startling emerald eyes fell onto Kaidan and she froze up. Her barrier fizzled out and a sharp gasp escaped her lips before she located her voice again. "Kaidan...? But... you died. You were on Virmire when..." She trailed off into silence before John stepped forward, ensuring Kaidan was ever so slightly behind himself. Neither human spectre was wearing their armor and with a human biotic on their hands, and possibly a crazy one at that, it was not a comfortable position to be in.   
"My name is John Shepard, Spectre and Commander of the Alliance Navy. I don't know who you are, or why you look like some long lost sister of mine, but I'd like to know what the hell you're doing on my ship and why you're accusing my boyfriend of being dead." John stated in that serious, cold tone he often used with politicians and enemies alike. The woman, Jane, gave him a surprised look before she shuddered.   
"Joker!" She finally yelled before bolting for the door. John drew his side arm but Kaidan stopped him just before he could shoot the woman.   
"Commander, wait! She's probably not exactly mentally sound, and that aside I've got the feeling that she might be serious. I don't think she's lying, and she's terrified. Shooting at her will only cement her fears, though." Kaidan said quickly as the woman's shouts cut off when she presumably reached the elevators. "Besides, I'm sure Joker can handle a hysterical woman. I hope." 

~~**~~**~~**~~

It took some time but Joker did manage to calm Jane down, but she kept hugging him, which in turn caused the pilot to have a mild panic attack each time. Sure, this woman acted like she was the commander of this ship, even knew intimate details of his past that only John would know himself, but she was acting like Joker was more than just her friend and co worker at the same time. When John and Kaidan finally approached them in the cock pit Shepard did more than throw a barrier around herself and Joker, no, she threw a barrier around the entire cock pit to keep them out. Joker seemed impressed, and Kaidan couldn't even break the barrier down, which left them to talk through it while Jane stayed parked in to co pilot seat like she was born to take that position. The more they talked the more information they learned. Apparently Jane had been on the Normandy SR2 and in the middle of a suicide mission to take down the collectors. She'd been on her way to Illium to recruit a Drell assassin named Thane for their cause when the ship encountered a Wormhole that they couldn't get away from. All of this sounded familiar save for the different time lines. Just like John, Jane was a colony kid who lost her parents in a raid and then also lost her whole squad on Mindior during a Thresher Maw attack. However, unlike John, she'd chosen to sacrifice Kaidan on Virmire and saved Ashley instead. She'd also developed an intimate relationship with Joker after the encounter with Ashley on Horizon. Once everything was explained John gave Joker a look before the man could tell Jane that he didn't see her like that, at all. She was already showing signs of shock, having her only save person tell her that was a bad idea. Instead she was escorted down to medical by Garrus and John was left trying to figure out what to do. Jane was pretty much a female version of him though, and with no other alternative and a Reaper war on the horizon they decided to keep her on the ship until they had a better solution. When they reported this incident to Hackett the guy was more than happy to have a 'Second Shepard' around to help and Anderson just laughed at him. She took up post as Joker's co-pilot once the doctor cleared her for duty and things calmed down for the most part. 

~~**~~**~~**~~

"You know, I can't believe I haven't noticed til now that you're wearing makeup." Joker stated with surprise in his tone one day during Alpha shift. Jane blinked in surprise before looking away from her HUD and met his eyes. "It's real subtle, too, enough so that it takes some real close inspection to see but it's there." He added as an after note and he raised an eyebrow at the slight flush that rose to her cheeks before she grinned brightly. It made his heart skip a beat because of how damn young it made her look, too.   
"You know, it took me dying and Cerberus bring me back again for you to realize that in my universe too. You were so shocked that you kept swearing that I only started doing it after I was brought back from the dead too, claiming that my scars were making me self conscious and that it was silly of me to do that." She chirped before glancing back to her HUD. "Without my makeup my scars do show more, though." She admitted softly and Joker clucked his tongue.   
"Your scars aren't a bad thing, Shepard. They show that you're a survivor." Joker huffed with a slight pout and Jane's eyes softened.   
"Tell you what, I'll wash my make up off before next shift. Then you can tell me if my scars aren't bad." She offered and they made it a deal. When next shift started EDI sung by in her new body only to pause when she saw an unnatural red glow around the co-pilot area. When she voiced her concern about it Jane turned to look at her and there were thin cracks along her face where the cybernetic implants Cerberus put in here were showing through her epidermal layers and the AI froze up in shock. John had never shown signs of this deterioration but when Jane noticed the reaction her expression instantly went distant and icy before she glared at EDI and went back to work. Joker subtly motioned for the AI to go back to patrolling the ship before Shepard got any more upset. 

~~**~~**~~**~~

"So, Loco, what do you think about Lola now that it's been a few days?" James asked when John sung by his station while he was doing pull ups, like he did every morning before attending his duties. John admired the other man's form for a moment before he even thought about replying.   
"She's certainly interesting to be sure. She told me her scars only began to appear when she began to crack under the pressures of her suicide mission. Dr. Chakwas backed her up with the theory that negative mind sets will cause my body, and hers, to reject the implants and create scarring. She laughed when the Doctor suggested she think more positively, though." John replied honestly and James chuckled before dropping to the floor.   
"You should've seen her when she was sparring with me yesterday. She was tough, and didn't even hold back like you did when we went at each other. Ruthless is how I'd discribe her." James huffed before turning to face his commander and offering a lopsided smirk. "Have you seen her talking to Joker? He's starting to fall for her, man, and he's falling hard. As much as he's trying to keep himself distanced he's loosing serious ground. Did you know EDI says he's the reason she showed her scars in the first place? Apparently she'd worn make up to hide it but he convinced her to wash it off and be proud of how she really looks. His reaction must've made her more confident because she hasn't hidden 'em since." James rambled and John raised an eyebrow before humming thoughtfully.   
"I wonder... maybe we should glue them together. She seems unstable even at the best of times, but if he can keep her grounded than she shouldn't pose any sort of risk to the ship or crew. It does make me curious about what happened to her to make her act so differently, though. It can't have been just Virmire, it had to be something else too." John murmured before he took his leave. He'd talk to Kaidan next and then probably visit Jane.


	2. First Mission

**Summary for the Chapter:**

> John Shepard takes Jane Shepard on the first ground mission since she'd arrived on his ship to see how she can lead a team of two other members from his crew.

Jane was reluctant at first when John had proposed she lead a ground team on the next mission they went to. Apparently there was a biotic school for the most talented children with a suspicious signal coming from it so John wanted to check it out. He claimed that they could find the source faster with two ground teams but she was fast to call him on his bull shit, stating he wanted to see if she could lead as well as he could. They argued and nearly came to blows before they settled on an agreement. Jane would go, sure, but she got to pick the two crew members she took with her. She was apparently a biotic sentinel, like Kaidan, so she strategically chose people who would compliment her abilities. She picked Garrus since he had the combat training she lacked, and then added Javik since he was a pure biotic and had abilities in that field that she lacked. At first the Prothian argued about following her lead but there must've been something in the look she shot him because his arguments quickly ceased. Everyone suited up and entered the shuttle. 

~~**~~**~~**~~

"You know, Javik, if you keep bitching to the Commander I'm pretty sure she'll deck you and wipe the floors of this station with your face in about five seconds." Garrus warned seriously after Javik once again mentioned that Shepard's shoot first and ask later approach was going to turn around and bite them sooner rather than later. The station had an upper level that went across the whole area, so Jane took the upper level while John handled the lower one, staying unseen while supplying back up when needed. She heard them over her helmet's comm system and turned around, eyes red and glowing from her implants. 

"Oh, I'll do more than just wipe the floor with your face, Prothian. I've had just about enough of your insubordination. I may not be the Shepard you're used to taking orders from but I will not hesitate to put a bullet in your brain if I so much as suspect that you're going to try something funny." Shepard snapped in a hostile tone. Garrus seemed taken a back but when Javik looked at him the Turian quickly took a step back to make it more than clear that the guy was on his own. 

"Understood, Commander." Javik finally huffed and Jane glared at him for a moment before she saw movement off to her left. Before her two team mates even saw what made it she dropped to one knee and threw a biotic pull at the source, dragging a Cerberus soldier from cover. She looked caught off guard, since she was supposed to be with Cerberus, but when the man looked up and saw her he drew his gun, forcing her to pull her pistol and fire. She got a head shot first try and Garrus cleared his throat nervously. 

"I take it John didn't warn you, then. Cerberus has been trying to kill us along with the Reapers, Shepard, sorry that you didn't know that before heading in here." Garrus explained while Jane stood up. She said nothing, merely approached the corpse and kicked the gun out of its hand. She fired two more shots in its head just to make sure it wouldn't get up and gestured for them to follow before moving forward. The silence from here was more chilling than any other reaction would've been. 

~~**~~**~~**~~

"I warned you about Cerberus, dammit!" Jack yelled before bitch slapping John immediately after having teased him about being King of the Boy-scouts. Jane tilted her head before coming out of cover and hopping down to where they were talking. She used that fancy trick that most Asari could pull off to avoid landing wrong and holstered her weapon. Jack spun, biotics already active but blinked in surprise when she saw Jane. 

"As much as I've wanted to slap that man for some time now, how about an introduction? I'm Jane Shepard, and it's a long story as to why I'm here. What I want to know, however, is what you told John about Cerberus." She purred before sliding her helmet off so Jack could see the intense scarring that seemed to have gotten worse the more time she'd spent in their universe. "I know you've told me more than your fair share already, but something seems to have changed when I wasn't looking." Jack looked her up and down and when John just shrugged Jack smirked and dragged Jane off, claiming that they needed a 'girl talk' while John searched for a way to open the doors leading to the rest of the facility. 

~~**~~**~~**~~

Only once the students, Jack, and what's-her-name who was likely some old sweet heart of Anderson's was safely on board the Normandy and the ship was on its way to the Citidel to drop them off did John confront Jane about what Jack had spoken to her about. She refused to talk about the subject and John was unwilling to test her patience by pushing it either. Jane visited Javik and asked if they'd have any further problems and when he said 'no' she took him for his word and returned to the cock pit to take her spot by Joker. Her hair was pulled back into a messy pony tail, allowing her to focus on her HUD before he finally broke the companionable silence between them. 

"Hey, Jane, Shepard told me that you seemed to be real tense during the ground mission. You feeling alright?" Joker asked and it took her a minute to realize that 'Shepard' meant he was referring to John. 

"Oh, that. Yeah, I just... it's weird, being here. Apparently John already finished his suicide mission with the Collectors and while his whole team survived he also claims that no body had taken the Reaper threat seriously save for Anderson and Hackett. Nobody. So Earth was taken when they first invaded and now planet after planet is falling to them. I'm just questioning a lot of things now." She admitted and Joker turned over the controls to EDI, shutting down Jane's HUD in the process before he turned his chair to face her directly. 

"Jane, you knew after you defeated Sovereign that the Council would have its head too far up its ass to see the bigger problem. I mean, come on, when we reach the Citadel itself you'll realize just how desperate they are to lie to themselves and the people that live there in spite how many refugees have arrived by now." He sighed and she looked away from his earnest eyes before looking up, her expression soft in spite of the harsh lighting her cybernetics produced. 

"I saw you looking at news articles this morning while we were navigating that asteroid field. I looked it up later in the crew's quarters and I know about Tiptree, Joker. For what it's worth, I'm always here if you want to talk." She stated, both trying to shift the subject from herself and making it clear that she knew damn well that she wasn't the only one hurting. Joker was caught off guard at first before his own expression seemed to falter and he sighed. 

"It was gonna happen sooner or later, Jane, I already knew that. It just... maybe part of me was hoping the Reapers would over look a small colony like that." Joker murmured and she got up only to kneel beside Joker's chair and pull him into a hug, refusing to acknowledge the fact that the man was silently crying. They stayed like that for a while, letting EDI fly the ship while Jane held Joker in her arms, making soothing noises while he simply let her comfort him.


End file.
